Handwritten document-image binarization is a semantic segmentation process to differentiate ink pixels from background pixels. It is one of the essential steps towards character recognition, writer identification, and script-style evolution analysis. The binarization task itself is challenging due to the vast diversity of writing styles, inks, and paper materials. It is even more difficult for historical manuscripts due to the aging and degradation of the documents over time. One of such manuscripts is the Dead Sea Scrolls (DSS) image collection, which poses extreme challenges for the existing binarization techniques. This article proposes a new binarization technique for the DSS images using the deep encoder-decoder networks. Although the artificial neural network proposed here is primarily designed to binarize the DSS images, it can be trained on different manuscript collections as well. Additionally, the use of transfer learning makes the network already utilizable for a wide range of handwritten documents, making it a unique multi-purpose tool for binarization. Qualitative results and several quantitative comparisons using both historical manuscripts and datasets from handwritten document image binarization competition (H-DIBCO and DIBCO) exhibit the robustness and the effectiveness of the system. The best performing network architecture proposed here is a variant of the U-Net encoder-decoders.